PT - JOURNAL ARTICLE AU - Marijke Autenrieth AU - Stefanie Hartmann AU - Ljerka Lah AU - Anna Roos AU - Alice B. Dennis AU - Alice B. Dennis AU - Ralph Tiedemann TI - High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (<em>Phocoena phocoena</em>) AID - 10.1101/246173 DP - 2018 Jan 01 TA - bioRxiv PG - 246173 4099 - http://biorxiv.org/content/early/2018/04/18/246173.short 4100 - http://biorxiv.org/content/early/2018/04/18/246173.full AB - The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found in waters across the Northern hemisphere. It occurs in coastal water and inhabits water basins that vary broadly in salinity, temperature, and food availability. These diverse habitats could drive differentiation among populations; population structure within the north Atlantic (north of 51° latitude) is not fully resolved, particularly in relation to Baltic Sea populations. Here we report the first harbour porpoise genome, assembled de novo from a Swedish Kattegat individual. The genome is one of the most complete cetacean genomes currently available, with a total size of 2.7 Gb, and 50% of the total length found in just 34 scaffolds. Using the largest scaffolds, we were able to examine chromosome-level rearrangements relative to the genome of the closest related species available, domestic cattle (Bos taurus). The draft annotation comprises 22,154 predicted gene models, which we further annotated through matches to NCBI nucleotide database, GO categorization, and motif prediction. To infer the adaptive abilities of this species, as well as their population history, we performed Bayesian skyline analysis of the genome, which is concordant with the demographic history of this species, including expansion and fragmentation events. Overall, this genome assembly, together with the draft annotation, represents a crucial addition to the limited genetic markers currently available for the study of porpoise and cetacean conservation, phylogeny, and evolution.